Commit e59ec7f7 authored by Midoux Cedric's avatar Midoux Cedric
Browse files

Table/digestomics.tsv

parent a90eabb3
......@@ -83,3 +83,27 @@ with open("user_ko-sort.txt", "r") as f:
old_ko=ko
out.write("%s\t%s\n"%(gene, ko))
```
## Final table
```bash
join -t $'\t' report/count-genes_FGS-J80_A-coassembly.tsv report/count-genes_FGS-J80_B-coassembly.tsv | \
join -t $'\t' - report/count-genes_FGS-J177_A-coassembly.tsv | \
join -t $'\t' - report/count-genes_FGS-J177_B-coassembly.tsv | \
sort -k1,1 \
> Table/count-genes_coassembly.tsv
awk -F $'\t' -v OFS=$'\t' '{if($1=="C") print $2,$3,$4 ; else print $2,$3,"NA; NA; NA; NA; NA; NA; NA;"}' report/genes_coassembly-taxNames.tsv | \
sort -k1,1 \
> Table/taxName_coassembly.tsv
sort -k2,2 work/ghostKOALA/user_ko-uniq.txt | \
join --check-order -t $'\t' -e NA -a1 -12 -21 -o 1.1,0,2.2 - work/ghostKOALA/KO_name.txt | \
sort -k1,1 \
> Table/KO_coassembly.tsv
echo -e "J80_A\tJ80_B\tJ177_A\tJ177_B\ttaxID_kaijuNR\ttaxID_name\tKO_ghostKOALA\tKO_name"> Table/digestomics.tsv
join --check-order -t $'\t' -e NA -a1 Table/count-genes_coassembly.tsv Table/taxName_coassembly.tsv | \
join --check-order -t $'\t' -e NA -a1 - Table/KO_coassembly.tsv \
>> Table/digestomics.tsv
```
\ No newline at end of file
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